Studying Superbugs – Juliette Hayer on Baargin JOSSCast: Open Source for Researchers

#3: Juliette Hayer joins Arfon and Abby to discuss Baargin, an open source tool she created to analyze bacterial genomes, especially those resistant to antibiotics.

Juliette is a PhD Researcher at the French Research
Institute for Sustainable Development (IRD, Institut de Recherche pour le Développement), at the MIVEGEC research unit, where she implements computational biology methods for bacterial genomics and metagenomics to understand the circulation and transmission of antimicrobial resistance.

You can find Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer).

Episode Highlights


[00:02:21] Introduction to Baargin: Juliette explains that Baargin
stands for Bacterial Assembly and Antimicrobial Resistance Genes
Detection in Nextflow. She developed it to analyze the genomes of
drug-resistant bacteria in various environments.
[00:06:20] Multiplex Sequencing: Juliette discusses the challenge of
assembling genomes for multiple strains simultaneously using
high-throughput sequencing technologies.
[00:07:21] Next-Gen Sequencing and Assembly: The conversation delves
into next-generation sequencing, the assembly of short reads, and the
emergence of long-read technologies for comprehensive genome analysis.
[00:09:59] Target Audience: Juliette identifies microbiologists as
the primary audience for Baargin, emphasizing its user-friendliness for
researchers producing genome data.
[00:12:50] Nextflow in Bioinformatics: Juliette explains the role of
Nextflow in bioinformatics and its popularity, highlighting its
benefits for scalable and reproducible workflows.
[00:17:03] Open Source Philosophy: Juliette shares her commitment to
open source principles, advocating for transparency, reproducibility,
and collaborative contributions in research.
[00:19:20] Research Using Baargin: Juliette discusses her published
studies, including the identification of drug-resistant E. coli
transmission in Chile and ongoing projects in Vietnam and Cambodia.
[00:20:14] Publishing in JOSS: Juliette describes the benefits of
publishing in the Journal of Open Source Software (JOSS), emphasizing
the focus on code and transparent review processes.
[00:23:27] Documentation Importance: The hosts discuss the
significance of documentation in software development, with Juliette
highlighting its critical role in ensuring usability.
[00:26:03] Contributions and Skills: Juliette welcomes contributions
to Baargin, mentioning that comfort with git and Nextflow is essential
for potential contributors.
[00:28:27] Future Roadmap: Juliette outlines plans for extending
Baargin, including adding tools for predicting resistance genes,
improving detection of mobile genetic elements, and enhancing
multi-locus sequence typing.

Links


JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05397
Baargin code repository: https://github.com/jhayer/baargin
Nextflow: https://www.nextflow.io/
Study using Baargin: Multiple clonal transmissions of clinically
relevant extended-spectrum beta-lactamase–producing Escherichia coli
among livestock, dogs, and wildlife in Chile: https://doi.org/10.1016/j.jgar.2023.07.009
Juliette on GitHub (@jhayer), ResearchGate, and X (@juliette_hayer).
The Journal of Open Source Software (Twitter/X, blog)
@arfon on (fosstodon, Linkedin, GitHub, website)
@abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website)